Bioconductor Ashr

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DESeq2 apeglm DESeq ApeGLM Ashr

updated 19 months ago by Michael Love 43k • written 19 months ago by Ndimensional ▴ 20

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Ashr LFCShrinkage IHW DESeq2

3.2 years ago • updated 3.1 years ago Bex • 0

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ashr DESeq2 apeglm

updated 3.5 years ago by Michael Love 43k • written 3.6 years ago by Guandong Shang ▴ 40

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ashr DESeq2 lfcShrink svalue

4.0 years ago Enrico • 0

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deseq2 ashr

4.4 years ago da.de ▴ 30

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deseq2 ashr rna-seq

4.8 years ago Alex • 0

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821

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ashr

4.8 years ago kavator ▴ 30

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ashr Deseq2 lfcThreshold

updated 3.4 years ago by Michael Love 43k • written 4.9 years ago by Iryna • 0

8 results • Page 1 of 1

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Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k

If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…

Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0

why aren't there any answers?

Comment: Too many significant genes when integrating gtex and tcga by Jane • 0

I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…

Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180

Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…

Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k

No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…

Votes

A: Unbalanced experiment with multiple samples from each patient.

Unbalanced experiment with multiple samples from each patient.

Answer: Vertical line at A=0, nothing else, on MA plot

Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct

Answer: Group-specific condition effects with individuals nested: matrix is not full ra

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